Multiple sequence alignment - TraesCS6B01G271500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS6B01G271500 chr6B 100.000 3266 0 0 1 3266 489716037 489712772 0.000000e+00 6032.0
1 TraesCS6B01G271500 chr6B 75.180 278 45 12 108 364 497783106 497783380 3.450000e-20 110.0
2 TraesCS6B01G271500 chr6A 95.077 2458 93 15 504 2938 470212345 470214797 0.000000e+00 3843.0
3 TraesCS6B01G271500 chr6A 94.048 252 14 1 3016 3266 470214806 470215057 6.610000e-102 381.0
4 TraesCS6B01G271500 chr6D 94.828 2301 80 12 634 2906 331254902 331257191 0.000000e+00 3554.0
5 TraesCS6B01G271500 chr6D 97.573 206 4 1 3027 3232 331258520 331258724 5.180000e-93 351.0
6 TraesCS6B01G271500 chr6D 91.549 213 12 5 425 632 331254519 331254730 4.120000e-74 289.0
7 TraesCS6B01G271500 chr6D 95.050 101 5 0 2892 2992 331258414 331258514 3.370000e-35 159.0
8 TraesCS6B01G271500 chr6D 78.136 279 34 18 109 362 245463103 245462827 5.640000e-33 152.0
9 TraesCS6B01G271500 chr6D 95.745 47 2 0 103 149 144603147 144603193 3.490000e-10 76.8
10 TraesCS6B01G271500 chr2B 84.452 1177 165 16 997 2161 607106567 607107737 0.000000e+00 1144.0
11 TraesCS6B01G271500 chr2D 84.354 1176 168 15 997 2161 515630051 515631221 0.000000e+00 1138.0
12 TraesCS6B01G271500 chr2A 83.759 1176 175 14 997 2161 659323646 659324816 0.000000e+00 1099.0
13 TraesCS6B01G271500 chr7A 78.495 279 33 7 107 360 24763660 24763384 1.210000e-34 158.0
14 TraesCS6B01G271500 chr7A 77.419 279 39 3 106 360 681096721 681096443 9.440000e-31 145.0
15 TraesCS6B01G271500 chr4A 77.061 279 37 13 107 360 117706796 117706520 5.680000e-28 135.0
16 TraesCS6B01G271500 chr5A 76.344 279 42 18 109 363 494225070 494225348 9.510000e-26 128.0
17 TraesCS6B01G271500 chr1B 76.596 282 35 15 106 360 317200777 317201054 3.420000e-25 126.0
18 TraesCS6B01G271500 chr1B 75.347 288 45 13 101 363 54167034 54166748 7.410000e-22 115.0
19 TraesCS6B01G271500 chr5B 77.155 232 37 6 147 364 686826400 686826629 1.590000e-23 121.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G271500 chr6B 489712772 489716037 3265 True 6032.00 6032 100.0000 1 3266 1 chr6B.!!$R1 3265
1 TraesCS6B01G271500 chr6A 470212345 470215057 2712 False 2112.00 3843 94.5625 504 3266 2 chr6A.!!$F1 2762
2 TraesCS6B01G271500 chr6D 331254519 331258724 4205 False 1088.25 3554 94.7500 425 3232 4 chr6D.!!$F2 2807
3 TraesCS6B01G271500 chr2B 607106567 607107737 1170 False 1144.00 1144 84.4520 997 2161 1 chr2B.!!$F1 1164
4 TraesCS6B01G271500 chr2D 515630051 515631221 1170 False 1138.00 1138 84.3540 997 2161 1 chr2D.!!$F1 1164
5 TraesCS6B01G271500 chr2A 659323646 659324816 1170 False 1099.00 1099 83.7590 997 2161 1 chr2A.!!$F1 1164

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
614 619 0.168128 GTGGTGGTCAAACGCATAGC 59.832 55.0 0.0 0.0 0.0 2.97 F
1719 1932 0.260816 AGGGCGTCTGTATGGTCCTA 59.739 55.0 0.0 0.0 0.0 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1737 1950 1.497991 CGAACTTCTTCTTGTCCGCA 58.502 50.0 0.0 0.0 0.00 5.69 R
3244 4715 0.661483 GACGTTCTGCTTTTGCCTGC 60.661 55.0 0.0 0.0 46.87 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
39 40 9.917129 AGTAATAAATAAAAACCAAAACGGGAG 57.083 29.630 0.00 0.00 40.22 4.30
40 41 9.911138 GTAATAAATAAAAACCAAAACGGGAGA 57.089 29.630 0.00 0.00 40.22 3.71
42 43 6.718522 AAATAAAAACCAAAACGGGAGAGA 57.281 33.333 0.00 0.00 40.22 3.10
43 44 5.959618 ATAAAAACCAAAACGGGAGAGAG 57.040 39.130 0.00 0.00 40.22 3.20
44 45 1.605753 AAACCAAAACGGGAGAGAGC 58.394 50.000 0.00 0.00 40.22 4.09
45 46 0.602905 AACCAAAACGGGAGAGAGCG 60.603 55.000 0.00 0.00 40.22 5.03
46 47 1.004918 CCAAAACGGGAGAGAGCGT 60.005 57.895 0.00 0.00 0.00 5.07
47 48 0.245539 CCAAAACGGGAGAGAGCGTA 59.754 55.000 0.00 0.00 0.00 4.42
48 49 1.134788 CCAAAACGGGAGAGAGCGTAT 60.135 52.381 0.00 0.00 0.00 3.06
49 50 1.927174 CAAAACGGGAGAGAGCGTATG 59.073 52.381 0.00 0.00 0.00 2.39
50 51 0.460311 AAACGGGAGAGAGCGTATGG 59.540 55.000 0.00 0.00 0.00 2.74
51 52 0.395311 AACGGGAGAGAGCGTATGGA 60.395 55.000 0.00 0.00 0.00 3.41
52 53 0.395311 ACGGGAGAGAGCGTATGGAA 60.395 55.000 0.00 0.00 0.00 3.53
53 54 0.744874 CGGGAGAGAGCGTATGGAAA 59.255 55.000 0.00 0.00 0.00 3.13
54 55 1.136305 CGGGAGAGAGCGTATGGAAAA 59.864 52.381 0.00 0.00 0.00 2.29
55 56 2.799917 CGGGAGAGAGCGTATGGAAAAG 60.800 54.545 0.00 0.00 0.00 2.27
56 57 2.431057 GGGAGAGAGCGTATGGAAAAGA 59.569 50.000 0.00 0.00 0.00 2.52
57 58 3.118738 GGGAGAGAGCGTATGGAAAAGAA 60.119 47.826 0.00 0.00 0.00 2.52
58 59 4.504858 GGAGAGAGCGTATGGAAAAGAAA 58.495 43.478 0.00 0.00 0.00 2.52
59 60 4.935808 GGAGAGAGCGTATGGAAAAGAAAA 59.064 41.667 0.00 0.00 0.00 2.29
60 61 5.411669 GGAGAGAGCGTATGGAAAAGAAAAA 59.588 40.000 0.00 0.00 0.00 1.94
78 79 2.887151 AAACAAGGGATGAGGTGAGG 57.113 50.000 0.00 0.00 0.00 3.86
79 80 0.329596 AACAAGGGATGAGGTGAGGC 59.670 55.000 0.00 0.00 0.00 4.70
80 81 0.842030 ACAAGGGATGAGGTGAGGCA 60.842 55.000 0.00 0.00 0.00 4.75
81 82 0.329261 CAAGGGATGAGGTGAGGCAA 59.671 55.000 0.00 0.00 0.00 4.52
82 83 1.075601 AAGGGATGAGGTGAGGCAAA 58.924 50.000 0.00 0.00 0.00 3.68
83 84 0.329596 AGGGATGAGGTGAGGCAAAC 59.670 55.000 0.00 0.00 0.00 2.93
84 85 0.681243 GGGATGAGGTGAGGCAAACC 60.681 60.000 0.58 0.58 38.03 3.27
99 100 5.468540 GGCAAACCTATCAACCTTCTTTT 57.531 39.130 0.00 0.00 0.00 2.27
100 101 5.470368 GGCAAACCTATCAACCTTCTTTTC 58.530 41.667 0.00 0.00 0.00 2.29
101 102 5.243954 GGCAAACCTATCAACCTTCTTTTCT 59.756 40.000 0.00 0.00 0.00 2.52
102 103 6.382608 GCAAACCTATCAACCTTCTTTTCTC 58.617 40.000 0.00 0.00 0.00 2.87
103 104 6.570571 GCAAACCTATCAACCTTCTTTTCTCC 60.571 42.308 0.00 0.00 0.00 3.71
104 105 5.180810 ACCTATCAACCTTCTTTTCTCCC 57.819 43.478 0.00 0.00 0.00 4.30
105 106 4.852697 ACCTATCAACCTTCTTTTCTCCCT 59.147 41.667 0.00 0.00 0.00 4.20
106 107 5.313506 ACCTATCAACCTTCTTTTCTCCCTT 59.686 40.000 0.00 0.00 0.00 3.95
107 108 6.183361 ACCTATCAACCTTCTTTTCTCCCTTT 60.183 38.462 0.00 0.00 0.00 3.11
108 109 6.721668 CCTATCAACCTTCTTTTCTCCCTTTT 59.278 38.462 0.00 0.00 0.00 2.27
109 110 7.888546 CCTATCAACCTTCTTTTCTCCCTTTTA 59.111 37.037 0.00 0.00 0.00 1.52
110 111 9.297037 CTATCAACCTTCTTTTCTCCCTTTTAA 57.703 33.333 0.00 0.00 0.00 1.52
111 112 7.582667 TCAACCTTCTTTTCTCCCTTTTAAG 57.417 36.000 0.00 0.00 0.00 1.85
112 113 7.123383 TCAACCTTCTTTTCTCCCTTTTAAGT 58.877 34.615 0.00 0.00 0.00 2.24
113 114 6.961360 ACCTTCTTTTCTCCCTTTTAAGTG 57.039 37.500 0.00 0.00 0.00 3.16
114 115 5.302059 ACCTTCTTTTCTCCCTTTTAAGTGC 59.698 40.000 0.00 0.00 0.00 4.40
115 116 5.301805 CCTTCTTTTCTCCCTTTTAAGTGCA 59.698 40.000 0.00 0.00 0.00 4.57
116 117 6.015095 CCTTCTTTTCTCCCTTTTAAGTGCAT 60.015 38.462 0.00 0.00 0.00 3.96
117 118 6.331369 TCTTTTCTCCCTTTTAAGTGCATG 57.669 37.500 0.00 0.00 0.00 4.06
118 119 5.833131 TCTTTTCTCCCTTTTAAGTGCATGT 59.167 36.000 0.00 0.00 0.00 3.21
119 120 7.001674 TCTTTTCTCCCTTTTAAGTGCATGTA 58.998 34.615 0.00 0.00 0.00 2.29
120 121 6.569179 TTTCTCCCTTTTAAGTGCATGTAC 57.431 37.500 5.71 5.71 0.00 2.90
121 122 5.235850 TCTCCCTTTTAAGTGCATGTACA 57.764 39.130 16.62 0.00 0.00 2.90
122 123 5.626142 TCTCCCTTTTAAGTGCATGTACAA 58.374 37.500 16.62 0.00 0.00 2.41
123 124 6.245408 TCTCCCTTTTAAGTGCATGTACAAT 58.755 36.000 16.62 7.06 0.00 2.71
124 125 6.150976 TCTCCCTTTTAAGTGCATGTACAATG 59.849 38.462 16.62 4.44 0.00 2.82
125 126 5.184864 TCCCTTTTAAGTGCATGTACAATGG 59.815 40.000 16.62 12.11 0.00 3.16
126 127 5.047377 CCCTTTTAAGTGCATGTACAATGGT 60.047 40.000 16.62 0.00 0.00 3.55
127 128 6.454795 CCTTTTAAGTGCATGTACAATGGTT 58.545 36.000 16.62 3.84 0.00 3.67
128 129 6.365789 CCTTTTAAGTGCATGTACAATGGTTG 59.634 38.462 16.62 0.00 0.00 3.77
129 130 6.641169 TTTAAGTGCATGTACAATGGTTGA 57.359 33.333 16.62 0.00 0.00 3.18
130 131 6.832520 TTAAGTGCATGTACAATGGTTGAT 57.167 33.333 16.62 0.00 0.00 2.57
131 132 7.929941 TTAAGTGCATGTACAATGGTTGATA 57.070 32.000 16.62 0.00 0.00 2.15
132 133 6.832520 AAGTGCATGTACAATGGTTGATAA 57.167 33.333 16.62 0.00 0.00 1.75
133 134 6.441093 AGTGCATGTACAATGGTTGATAAG 57.559 37.500 16.62 0.00 0.00 1.73
134 135 6.179756 AGTGCATGTACAATGGTTGATAAGA 58.820 36.000 16.62 0.00 0.00 2.10
135 136 6.094048 AGTGCATGTACAATGGTTGATAAGAC 59.906 38.462 16.62 0.00 0.00 3.01
136 137 5.942826 TGCATGTACAATGGTTGATAAGACA 59.057 36.000 0.00 0.00 0.00 3.41
137 138 6.093909 TGCATGTACAATGGTTGATAAGACAG 59.906 38.462 0.00 0.00 0.00 3.51
138 139 6.094048 GCATGTACAATGGTTGATAAGACAGT 59.906 38.462 0.00 0.00 0.00 3.55
139 140 7.677276 GCATGTACAATGGTTGATAAGACAGTC 60.677 40.741 0.00 0.00 0.00 3.51
140 141 7.004555 TGTACAATGGTTGATAAGACAGTCT 57.995 36.000 0.00 0.00 0.00 3.24
141 142 7.450074 TGTACAATGGTTGATAAGACAGTCTT 58.550 34.615 19.81 19.81 40.35 3.01
142 143 8.590204 TGTACAATGGTTGATAAGACAGTCTTA 58.410 33.333 22.68 22.68 42.49 2.10
237 238 9.214957 AGATATTCGTAAAAACATGTTGAGACA 57.785 29.630 12.82 0.00 40.71 3.41
242 243 9.605955 TTCGTAAAAACATGTTGAGACATATTG 57.394 29.630 12.82 0.00 44.55 1.90
243 244 8.779303 TCGTAAAAACATGTTGAGACATATTGT 58.221 29.630 12.82 0.00 44.55 2.71
244 245 8.839914 CGTAAAAACATGTTGAGACATATTGTG 58.160 33.333 12.82 0.00 44.55 3.33
245 246 9.677567 GTAAAAACATGTTGAGACATATTGTGT 57.322 29.630 12.82 0.00 44.55 3.72
250 251 9.897744 AACATGTTGAGACATATTGTGTTAAAG 57.102 29.630 11.07 0.00 44.55 1.85
251 252 8.514594 ACATGTTGAGACATATTGTGTTAAAGG 58.485 33.333 0.00 0.00 44.55 3.11
252 253 8.729756 CATGTTGAGACATATTGTGTTAAAGGA 58.270 33.333 0.00 0.00 44.55 3.36
253 254 8.862325 TGTTGAGACATATTGTGTTAAAGGAT 57.138 30.769 0.00 0.00 42.36 3.24
254 255 8.946085 TGTTGAGACATATTGTGTTAAAGGATC 58.054 33.333 0.00 0.00 42.36 3.36
255 256 8.946085 GTTGAGACATATTGTGTTAAAGGATCA 58.054 33.333 0.00 0.00 42.36 2.92
256 257 9.685276 TTGAGACATATTGTGTTAAAGGATCAT 57.315 29.630 0.00 0.00 42.36 2.45
257 258 9.330063 TGAGACATATTGTGTTAAAGGATCATC 57.670 33.333 0.00 0.00 42.36 2.92
258 259 9.553064 GAGACATATTGTGTTAAAGGATCATCT 57.447 33.333 0.00 0.00 42.36 2.90
259 260 9.553064 AGACATATTGTGTTAAAGGATCATCTC 57.447 33.333 0.00 0.00 42.36 2.75
260 261 9.553064 GACATATTGTGTTAAAGGATCATCTCT 57.447 33.333 0.00 0.00 42.36 3.10
261 262 9.911788 ACATATTGTGTTAAAGGATCATCTCTT 57.088 29.630 0.00 0.00 38.01 2.85
308 309 9.587772 TTTCTTATAATTTCTCTCTCTTCCACG 57.412 33.333 0.00 0.00 0.00 4.94
309 310 8.294954 TCTTATAATTTCTCTCTCTTCCACGT 57.705 34.615 0.00 0.00 0.00 4.49
310 311 8.407064 TCTTATAATTTCTCTCTCTTCCACGTC 58.593 37.037 0.00 0.00 0.00 4.34
311 312 4.873746 AATTTCTCTCTCTTCCACGTCA 57.126 40.909 0.00 0.00 0.00 4.35
312 313 4.873746 ATTTCTCTCTCTTCCACGTCAA 57.126 40.909 0.00 0.00 0.00 3.18
313 314 3.644884 TTCTCTCTCTTCCACGTCAAC 57.355 47.619 0.00 0.00 0.00 3.18
314 315 2.583143 TCTCTCTCTTCCACGTCAACA 58.417 47.619 0.00 0.00 0.00 3.33
315 316 3.157881 TCTCTCTCTTCCACGTCAACAT 58.842 45.455 0.00 0.00 0.00 2.71
316 317 3.574396 TCTCTCTCTTCCACGTCAACATT 59.426 43.478 0.00 0.00 0.00 2.71
317 318 4.039245 TCTCTCTCTTCCACGTCAACATTT 59.961 41.667 0.00 0.00 0.00 2.32
318 319 5.243060 TCTCTCTCTTCCACGTCAACATTTA 59.757 40.000 0.00 0.00 0.00 1.40
319 320 6.037786 TCTCTCTTCCACGTCAACATTTAT 57.962 37.500 0.00 0.00 0.00 1.40
320 321 6.100004 TCTCTCTTCCACGTCAACATTTATC 58.900 40.000 0.00 0.00 0.00 1.75
321 322 5.175859 TCTCTTCCACGTCAACATTTATCC 58.824 41.667 0.00 0.00 0.00 2.59
322 323 5.046591 TCTCTTCCACGTCAACATTTATCCT 60.047 40.000 0.00 0.00 0.00 3.24
323 324 6.153851 TCTCTTCCACGTCAACATTTATCCTA 59.846 38.462 0.00 0.00 0.00 2.94
324 325 6.884832 TCTTCCACGTCAACATTTATCCTAT 58.115 36.000 0.00 0.00 0.00 2.57
325 326 7.335627 TCTTCCACGTCAACATTTATCCTATT 58.664 34.615 0.00 0.00 0.00 1.73
326 327 6.918892 TCCACGTCAACATTTATCCTATTG 57.081 37.500 0.00 0.00 0.00 1.90
327 328 6.645306 TCCACGTCAACATTTATCCTATTGA 58.355 36.000 0.00 0.00 0.00 2.57
328 329 6.537301 TCCACGTCAACATTTATCCTATTGAC 59.463 38.462 5.53 5.53 43.62 3.18
329 330 6.315144 CCACGTCAACATTTATCCTATTGACA 59.685 38.462 13.91 0.00 46.09 3.58
330 331 7.012327 CCACGTCAACATTTATCCTATTGACAT 59.988 37.037 13.91 0.00 46.09 3.06
331 332 8.064222 CACGTCAACATTTATCCTATTGACATC 58.936 37.037 13.91 0.00 46.09 3.06
332 333 7.768582 ACGTCAACATTTATCCTATTGACATCA 59.231 33.333 13.91 0.00 46.09 3.07
333 334 8.064222 CGTCAACATTTATCCTATTGACATCAC 58.936 37.037 13.91 0.00 46.09 3.06
334 335 9.113838 GTCAACATTTATCCTATTGACATCACT 57.886 33.333 9.84 0.00 45.43 3.41
345 346 9.298250 TCCTATTGACATCACTAAGATACTACC 57.702 37.037 0.00 0.00 34.43 3.18
346 347 9.078990 CCTATTGACATCACTAAGATACTACCA 57.921 37.037 0.00 0.00 34.43 3.25
349 350 9.770097 ATTGACATCACTAAGATACTACCATTG 57.230 33.333 0.00 0.00 34.43 2.82
350 351 8.306313 TGACATCACTAAGATACTACCATTGT 57.694 34.615 0.00 0.00 34.43 2.71
351 352 9.416284 TGACATCACTAAGATACTACCATTGTA 57.584 33.333 0.00 0.00 34.43 2.41
352 353 9.680315 GACATCACTAAGATACTACCATTGTAC 57.320 37.037 0.00 0.00 34.43 2.90
353 354 9.197306 ACATCACTAAGATACTACCATTGTACA 57.803 33.333 0.00 0.00 34.43 2.90
356 357 9.197306 TCACTAAGATACTACCATTGTACATGT 57.803 33.333 2.69 2.69 0.00 3.21
357 358 9.464714 CACTAAGATACTACCATTGTACATGTC 57.535 37.037 0.00 0.00 0.00 3.06
358 359 8.639761 ACTAAGATACTACCATTGTACATGTCC 58.360 37.037 0.00 0.00 0.00 4.02
359 360 7.676683 AAGATACTACCATTGTACATGTCCT 57.323 36.000 0.00 0.00 0.00 3.85
360 361 8.777578 AAGATACTACCATTGTACATGTCCTA 57.222 34.615 0.00 0.00 0.00 2.94
361 362 8.777578 AGATACTACCATTGTACATGTCCTAA 57.222 34.615 0.00 0.00 0.00 2.69
362 363 9.381038 AGATACTACCATTGTACATGTCCTAAT 57.619 33.333 0.00 0.00 0.00 1.73
365 366 8.548880 ACTACCATTGTACATGTCCTAATAGT 57.451 34.615 0.00 4.03 0.00 2.12
366 367 8.421784 ACTACCATTGTACATGTCCTAATAGTG 58.578 37.037 0.00 0.00 0.00 2.74
367 368 6.055588 ACCATTGTACATGTCCTAATAGTGC 58.944 40.000 0.00 0.00 0.00 4.40
368 369 6.126768 ACCATTGTACATGTCCTAATAGTGCT 60.127 38.462 0.00 0.00 0.00 4.40
369 370 6.425114 CCATTGTACATGTCCTAATAGTGCTC 59.575 42.308 0.00 0.00 0.00 4.26
370 371 6.791867 TTGTACATGTCCTAATAGTGCTCT 57.208 37.500 0.00 0.00 0.00 4.09
371 372 6.149129 TGTACATGTCCTAATAGTGCTCTG 57.851 41.667 0.00 0.00 0.00 3.35
372 373 5.656859 TGTACATGTCCTAATAGTGCTCTGT 59.343 40.000 0.00 0.00 0.00 3.41
373 374 5.683876 ACATGTCCTAATAGTGCTCTGTT 57.316 39.130 0.00 3.25 0.00 3.16
374 375 5.665459 ACATGTCCTAATAGTGCTCTGTTC 58.335 41.667 0.73 0.00 0.00 3.18
375 376 5.187772 ACATGTCCTAATAGTGCTCTGTTCA 59.812 40.000 0.73 0.00 0.00 3.18
376 377 5.939764 TGTCCTAATAGTGCTCTGTTCAT 57.060 39.130 0.73 0.00 0.00 2.57
377 378 6.299805 TGTCCTAATAGTGCTCTGTTCATT 57.700 37.500 0.73 0.00 0.00 2.57
378 379 7.418337 TGTCCTAATAGTGCTCTGTTCATTA 57.582 36.000 0.73 0.00 0.00 1.90
379 380 8.023021 TGTCCTAATAGTGCTCTGTTCATTAT 57.977 34.615 0.73 0.00 0.00 1.28
380 381 7.928167 TGTCCTAATAGTGCTCTGTTCATTATG 59.072 37.037 0.73 0.00 0.00 1.90
381 382 8.144478 GTCCTAATAGTGCTCTGTTCATTATGA 58.856 37.037 0.73 0.00 0.00 2.15
382 383 8.363390 TCCTAATAGTGCTCTGTTCATTATGAG 58.637 37.037 0.73 0.00 0.00 2.90
383 384 8.147058 CCTAATAGTGCTCTGTTCATTATGAGT 58.853 37.037 0.73 0.00 0.00 3.41
406 407 9.939047 GAGTATATAATCGAATTTTAGTGTGCG 57.061 33.333 0.00 0.00 0.00 5.34
407 408 9.472361 AGTATATAATCGAATTTTAGTGTGCGT 57.528 29.630 0.00 0.00 0.00 5.24
410 411 5.351233 AATCGAATTTTAGTGTGCGTTCA 57.649 34.783 0.00 0.00 0.00 3.18
411 412 4.123276 TCGAATTTTAGTGTGCGTTCAC 57.877 40.909 4.43 4.43 43.40 3.18
412 413 3.059461 TCGAATTTTAGTGTGCGTTCACC 60.059 43.478 8.11 0.00 42.46 4.02
413 414 3.561503 GAATTTTAGTGTGCGTTCACCC 58.438 45.455 8.11 0.00 42.46 4.61
414 415 2.039818 TTTTAGTGTGCGTTCACCCA 57.960 45.000 8.11 0.00 42.46 4.51
415 416 2.264005 TTTAGTGTGCGTTCACCCAT 57.736 45.000 8.11 0.00 42.46 4.00
416 417 2.264005 TTAGTGTGCGTTCACCCATT 57.736 45.000 8.11 0.00 42.46 3.16
417 418 2.264005 TAGTGTGCGTTCACCCATTT 57.736 45.000 8.11 0.00 42.46 2.32
418 419 0.951558 AGTGTGCGTTCACCCATTTC 59.048 50.000 8.11 0.00 42.46 2.17
419 420 0.665835 GTGTGCGTTCACCCATTTCA 59.334 50.000 1.69 0.00 42.46 2.69
420 421 1.066303 GTGTGCGTTCACCCATTTCAA 59.934 47.619 1.69 0.00 42.46 2.69
421 422 1.959985 TGTGCGTTCACCCATTTCAAT 59.040 42.857 0.00 0.00 42.46 2.57
422 423 2.363680 TGTGCGTTCACCCATTTCAATT 59.636 40.909 0.00 0.00 42.46 2.32
423 424 2.986479 GTGCGTTCACCCATTTCAATTC 59.014 45.455 0.00 0.00 37.24 2.17
427 428 4.798387 GCGTTCACCCATTTCAATTCATAC 59.202 41.667 0.00 0.00 0.00 2.39
466 468 9.886132 ACATTTTATAATAGTGAACGAAGGAGT 57.114 29.630 0.00 0.00 0.00 3.85
479 482 6.318144 TGAACGAAGGAGTACAGTAGATTAGG 59.682 42.308 0.00 0.00 0.00 2.69
489 492 3.194968 ACAGTAGATTAGGGAACACGTGG 59.805 47.826 21.57 1.66 0.00 4.94
613 618 0.442310 CGTGGTGGTCAAACGCATAG 59.558 55.000 0.00 0.00 0.00 2.23
614 619 0.168128 GTGGTGGTCAAACGCATAGC 59.832 55.000 0.00 0.00 0.00 2.97
616 621 0.878416 GGTGGTCAAACGCATAGCAA 59.122 50.000 0.00 0.00 0.00 3.91
617 622 1.472480 GGTGGTCAAACGCATAGCAAT 59.528 47.619 0.00 0.00 0.00 3.56
618 623 2.477863 GGTGGTCAAACGCATAGCAATC 60.478 50.000 0.00 0.00 0.00 2.67
632 638 5.467063 GCATAGCAATCTTTGGTAGGTACTC 59.533 44.000 11.27 0.00 45.58 2.59
786 979 6.347696 CATCCTCTTCTCTCTACAAAAGCAT 58.652 40.000 0.00 0.00 0.00 3.79
877 1072 4.409570 CGTTTTCTCTCGATACTTCCGAA 58.590 43.478 0.00 0.00 35.48 4.30
901 1102 1.486211 GGAGAGGAAGACGAATCCCA 58.514 55.000 0.00 0.00 37.71 4.37
904 1105 2.036604 GAGAGGAAGACGAATCCCATCC 59.963 54.545 0.00 0.00 37.71 3.51
946 1147 1.621992 TCTTCCGTCTCTCTGTTGCT 58.378 50.000 0.00 0.00 0.00 3.91
954 1155 0.590195 CTCTCTGTTGCTTGTGTGGC 59.410 55.000 0.00 0.00 0.00 5.01
986 1190 5.430220 TCGTCGTGTTAATTTCGATTCAG 57.570 39.130 0.00 0.00 36.08 3.02
1286 1496 1.898094 TCGACGACCACCCGAAGAA 60.898 57.895 0.00 0.00 0.00 2.52
1290 1500 1.738099 CGACCACCCGAAGAAGCTG 60.738 63.158 0.00 0.00 0.00 4.24
1389 1599 4.742201 GCCAGCTTCTGCGTCGGA 62.742 66.667 0.00 0.00 45.42 4.55
1485 1698 2.564947 CCCTAAGGCGCTCTTCATCTAT 59.435 50.000 7.64 0.00 36.93 1.98
1719 1932 0.260816 AGGGCGTCTGTATGGTCCTA 59.739 55.000 0.00 0.00 0.00 2.94
2390 2616 1.202627 GCGGATCAGAGAGGAATTGCT 60.203 52.381 0.00 0.00 0.00 3.91
2424 2650 5.920193 TTTGTTGATCTGGGAAATGGATC 57.080 39.130 0.00 0.00 37.11 3.36
2492 2719 7.950684 AGATACTACTAGTTGATTGGAGGCATA 59.049 37.037 11.43 0.00 0.00 3.14
2610 2837 4.828939 TGCATATGGAATGGATGAAAGGAC 59.171 41.667 4.56 0.00 0.00 3.85
2622 2849 3.896648 TGAAAGGACACGAATTTCAGC 57.103 42.857 0.00 0.00 37.86 4.26
2626 2853 5.471797 TGAAAGGACACGAATTTCAGCATTA 59.528 36.000 0.00 0.00 37.86 1.90
2635 2862 8.818057 ACACGAATTTCAGCATTATAGTTACTC 58.182 33.333 0.00 0.00 0.00 2.59
2639 2866 8.718102 AATTTCAGCATTATAGTTACTCGTGT 57.282 30.769 0.00 0.00 0.00 4.49
2727 2954 5.334879 GGACGACTTACATTGCTTGTCAAAT 60.335 40.000 0.00 0.00 39.87 2.32
2750 2977 4.277672 TCACCATTACGTGATACTCCTAGC 59.722 45.833 0.00 0.00 37.85 3.42
2751 2978 4.037565 CACCATTACGTGATACTCCTAGCA 59.962 45.833 0.00 0.00 35.68 3.49
2752 2979 4.833380 ACCATTACGTGATACTCCTAGCAT 59.167 41.667 0.00 0.00 0.00 3.79
2753 2980 6.008331 ACCATTACGTGATACTCCTAGCATA 58.992 40.000 0.00 0.00 0.00 3.14
2754 2981 6.492429 ACCATTACGTGATACTCCTAGCATAA 59.508 38.462 0.00 0.00 0.00 1.90
2755 2982 7.014905 ACCATTACGTGATACTCCTAGCATAAA 59.985 37.037 0.00 0.00 0.00 1.40
2818 3051 3.193479 AGCAACATAAGCTTGTAAAGGGC 59.807 43.478 9.86 4.34 46.35 5.19
2847 3080 9.503427 CGAAGGAATAAAATTGGAACTATGAAC 57.497 33.333 0.00 0.00 0.00 3.18
2866 3099 7.951530 ATGAACTGCTTTTATTTGACTTTGG 57.048 32.000 0.00 0.00 0.00 3.28
2870 3103 4.376146 TGCTTTTATTTGACTTTGGCCAC 58.624 39.130 3.88 0.00 0.00 5.01
2878 3111 2.023673 TGACTTTGGCCACTGTTTCAG 58.976 47.619 3.88 0.00 37.52 3.02
2900 4370 3.130340 GGACAGACATTCCTGAGAGAGTC 59.870 52.174 0.00 0.00 37.59 3.36
2997 4467 7.834881 TGGAACATTAGGAGTTCTCGTATAT 57.165 36.000 6.09 0.00 43.67 0.86
2998 4468 8.929260 TGGAACATTAGGAGTTCTCGTATATA 57.071 34.615 6.09 0.00 43.67 0.86
2999 4469 9.529823 TGGAACATTAGGAGTTCTCGTATATAT 57.470 33.333 6.09 0.00 43.67 0.86
3043 4513 5.335191 GGAGTTCTCATGACATGGTGTTTTC 60.335 44.000 15.37 6.84 0.00 2.29
3150 4621 1.753078 AGTAGCCCTGCGTGATCGA 60.753 57.895 0.00 0.00 39.71 3.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 9.917129 CTCCCGTTTTGGTTTTTATTTATTACT 57.083 29.630 0.00 0.00 35.15 2.24
14 15 9.911138 TCTCCCGTTTTGGTTTTTATTTATTAC 57.089 29.630 0.00 0.00 35.15 1.89
16 17 8.862085 TCTCTCCCGTTTTGGTTTTTATTTATT 58.138 29.630 0.00 0.00 35.15 1.40
17 18 8.411991 TCTCTCCCGTTTTGGTTTTTATTTAT 57.588 30.769 0.00 0.00 35.15 1.40
18 19 7.522562 GCTCTCTCCCGTTTTGGTTTTTATTTA 60.523 37.037 0.00 0.00 35.15 1.40
19 20 6.718522 TCTCTCCCGTTTTGGTTTTTATTT 57.281 33.333 0.00 0.00 35.15 1.40
20 21 5.278808 GCTCTCTCCCGTTTTGGTTTTTATT 60.279 40.000 0.00 0.00 35.15 1.40
21 22 4.217767 GCTCTCTCCCGTTTTGGTTTTTAT 59.782 41.667 0.00 0.00 35.15 1.40
22 23 3.566742 GCTCTCTCCCGTTTTGGTTTTTA 59.433 43.478 0.00 0.00 35.15 1.52
23 24 2.361119 GCTCTCTCCCGTTTTGGTTTTT 59.639 45.455 0.00 0.00 35.15 1.94
24 25 1.954382 GCTCTCTCCCGTTTTGGTTTT 59.046 47.619 0.00 0.00 35.15 2.43
25 26 1.605753 GCTCTCTCCCGTTTTGGTTT 58.394 50.000 0.00 0.00 35.15 3.27
26 27 0.602905 CGCTCTCTCCCGTTTTGGTT 60.603 55.000 0.00 0.00 35.15 3.67
27 28 1.004918 CGCTCTCTCCCGTTTTGGT 60.005 57.895 0.00 0.00 35.15 3.67
28 29 0.245539 TACGCTCTCTCCCGTTTTGG 59.754 55.000 0.00 0.00 38.75 3.28
29 30 1.927174 CATACGCTCTCTCCCGTTTTG 59.073 52.381 0.00 0.00 38.75 2.44
30 31 1.134788 CCATACGCTCTCTCCCGTTTT 60.135 52.381 0.00 0.00 38.75 2.43
31 32 0.460311 CCATACGCTCTCTCCCGTTT 59.540 55.000 0.00 0.00 38.75 3.60
32 33 0.395311 TCCATACGCTCTCTCCCGTT 60.395 55.000 0.00 0.00 38.75 4.44
33 34 0.395311 TTCCATACGCTCTCTCCCGT 60.395 55.000 0.00 0.00 41.11 5.28
34 35 0.744874 TTTCCATACGCTCTCTCCCG 59.255 55.000 0.00 0.00 0.00 5.14
35 36 2.431057 TCTTTTCCATACGCTCTCTCCC 59.569 50.000 0.00 0.00 0.00 4.30
36 37 3.802948 TCTTTTCCATACGCTCTCTCC 57.197 47.619 0.00 0.00 0.00 3.71
37 38 6.481954 TTTTTCTTTTCCATACGCTCTCTC 57.518 37.500 0.00 0.00 0.00 3.20
57 58 3.500343 CCTCACCTCATCCCTTGTTTTT 58.500 45.455 0.00 0.00 0.00 1.94
58 59 2.819348 GCCTCACCTCATCCCTTGTTTT 60.819 50.000 0.00 0.00 0.00 2.43
59 60 1.272147 GCCTCACCTCATCCCTTGTTT 60.272 52.381 0.00 0.00 0.00 2.83
60 61 0.329596 GCCTCACCTCATCCCTTGTT 59.670 55.000 0.00 0.00 0.00 2.83
61 62 0.842030 TGCCTCACCTCATCCCTTGT 60.842 55.000 0.00 0.00 0.00 3.16
62 63 0.329261 TTGCCTCACCTCATCCCTTG 59.671 55.000 0.00 0.00 0.00 3.61
63 64 1.075601 TTTGCCTCACCTCATCCCTT 58.924 50.000 0.00 0.00 0.00 3.95
64 65 0.329596 GTTTGCCTCACCTCATCCCT 59.670 55.000 0.00 0.00 0.00 4.20
65 66 0.681243 GGTTTGCCTCACCTCATCCC 60.681 60.000 0.00 0.00 0.00 3.85
66 67 0.329596 AGGTTTGCCTCACCTCATCC 59.670 55.000 0.00 0.00 41.08 3.51
67 68 3.118261 TGATAGGTTTGCCTCACCTCATC 60.118 47.826 1.95 5.63 44.08 2.92
68 69 2.846206 TGATAGGTTTGCCTCACCTCAT 59.154 45.455 1.95 0.00 44.08 2.90
69 70 2.265367 TGATAGGTTTGCCTCACCTCA 58.735 47.619 1.95 0.00 44.08 3.86
70 71 3.010420 GTTGATAGGTTTGCCTCACCTC 58.990 50.000 1.95 0.00 44.08 3.85
71 72 2.290960 GGTTGATAGGTTTGCCTCACCT 60.291 50.000 4.17 4.17 45.64 4.00
72 73 2.092323 GGTTGATAGGTTTGCCTCACC 58.908 52.381 0.00 0.00 45.64 4.02
73 74 3.073274 AGGTTGATAGGTTTGCCTCAC 57.927 47.619 0.00 0.00 45.64 3.51
74 75 3.330701 AGAAGGTTGATAGGTTTGCCTCA 59.669 43.478 0.00 0.00 45.64 3.86
75 76 3.956744 AGAAGGTTGATAGGTTTGCCTC 58.043 45.455 0.00 0.00 45.64 4.70
77 78 5.243954 AGAAAAGAAGGTTGATAGGTTTGCC 59.756 40.000 0.00 0.00 0.00 4.52
78 79 6.332735 AGAAAAGAAGGTTGATAGGTTTGC 57.667 37.500 0.00 0.00 0.00 3.68
79 80 6.071896 GGGAGAAAAGAAGGTTGATAGGTTTG 60.072 42.308 0.00 0.00 0.00 2.93
80 81 6.010850 GGGAGAAAAGAAGGTTGATAGGTTT 58.989 40.000 0.00 0.00 0.00 3.27
81 82 5.313506 AGGGAGAAAAGAAGGTTGATAGGTT 59.686 40.000 0.00 0.00 0.00 3.50
82 83 4.852697 AGGGAGAAAAGAAGGTTGATAGGT 59.147 41.667 0.00 0.00 0.00 3.08
83 84 5.443230 AGGGAGAAAAGAAGGTTGATAGG 57.557 43.478 0.00 0.00 0.00 2.57
84 85 7.767250 AAAAGGGAGAAAAGAAGGTTGATAG 57.233 36.000 0.00 0.00 0.00 2.08
85 86 9.297037 CTTAAAAGGGAGAAAAGAAGGTTGATA 57.703 33.333 0.00 0.00 0.00 2.15
86 87 7.785028 ACTTAAAAGGGAGAAAAGAAGGTTGAT 59.215 33.333 0.00 0.00 0.00 2.57
87 88 7.068226 CACTTAAAAGGGAGAAAAGAAGGTTGA 59.932 37.037 0.00 0.00 0.00 3.18
88 89 7.203218 CACTTAAAAGGGAGAAAAGAAGGTTG 58.797 38.462 0.00 0.00 0.00 3.77
89 90 6.183360 GCACTTAAAAGGGAGAAAAGAAGGTT 60.183 38.462 0.00 0.00 0.00 3.50
90 91 5.302059 GCACTTAAAAGGGAGAAAAGAAGGT 59.698 40.000 0.00 0.00 0.00 3.50
91 92 5.301805 TGCACTTAAAAGGGAGAAAAGAAGG 59.698 40.000 0.00 0.00 0.00 3.46
92 93 6.391227 TGCACTTAAAAGGGAGAAAAGAAG 57.609 37.500 0.00 0.00 0.00 2.85
93 94 6.323739 ACATGCACTTAAAAGGGAGAAAAGAA 59.676 34.615 0.00 0.00 0.00 2.52
94 95 5.833131 ACATGCACTTAAAAGGGAGAAAAGA 59.167 36.000 0.00 0.00 0.00 2.52
95 96 6.089249 ACATGCACTTAAAAGGGAGAAAAG 57.911 37.500 0.00 0.00 0.00 2.27
96 97 6.547880 TGTACATGCACTTAAAAGGGAGAAAA 59.452 34.615 0.00 0.00 0.00 2.29
97 98 6.065374 TGTACATGCACTTAAAAGGGAGAAA 58.935 36.000 0.00 0.00 0.00 2.52
98 99 5.626142 TGTACATGCACTTAAAAGGGAGAA 58.374 37.500 0.00 0.00 0.00 2.87
99 100 5.235850 TGTACATGCACTTAAAAGGGAGA 57.764 39.130 0.00 0.00 0.00 3.71
100 101 5.957842 TTGTACATGCACTTAAAAGGGAG 57.042 39.130 0.00 0.00 0.00 4.30
101 102 5.184864 CCATTGTACATGCACTTAAAAGGGA 59.815 40.000 0.00 0.00 0.00 4.20
102 103 5.047377 ACCATTGTACATGCACTTAAAAGGG 60.047 40.000 8.00 8.00 0.00 3.95
103 104 6.024552 ACCATTGTACATGCACTTAAAAGG 57.975 37.500 0.00 0.00 0.00 3.11
104 105 7.144661 TCAACCATTGTACATGCACTTAAAAG 58.855 34.615 0.00 0.00 0.00 2.27
105 106 7.043961 TCAACCATTGTACATGCACTTAAAA 57.956 32.000 0.00 0.00 0.00 1.52
106 107 6.641169 TCAACCATTGTACATGCACTTAAA 57.359 33.333 0.00 0.00 0.00 1.52
107 108 6.832520 ATCAACCATTGTACATGCACTTAA 57.167 33.333 0.00 0.00 0.00 1.85
108 109 7.826744 TCTTATCAACCATTGTACATGCACTTA 59.173 33.333 0.00 0.00 0.00 2.24
109 110 6.658816 TCTTATCAACCATTGTACATGCACTT 59.341 34.615 0.00 0.00 0.00 3.16
110 111 6.094048 GTCTTATCAACCATTGTACATGCACT 59.906 38.462 0.00 0.00 0.00 4.40
111 112 6.128035 TGTCTTATCAACCATTGTACATGCAC 60.128 38.462 0.00 0.00 0.00 4.57
112 113 5.942826 TGTCTTATCAACCATTGTACATGCA 59.057 36.000 0.00 0.00 0.00 3.96
113 114 6.094048 ACTGTCTTATCAACCATTGTACATGC 59.906 38.462 0.00 0.00 0.00 4.06
114 115 7.550551 AGACTGTCTTATCAACCATTGTACATG 59.449 37.037 4.06 0.00 0.00 3.21
115 116 7.624549 AGACTGTCTTATCAACCATTGTACAT 58.375 34.615 4.06 0.00 0.00 2.29
116 117 7.004555 AGACTGTCTTATCAACCATTGTACA 57.995 36.000 4.06 0.00 0.00 2.90
117 118 7.907214 AAGACTGTCTTATCAACCATTGTAC 57.093 36.000 20.85 0.00 34.42 2.90
211 212 9.214957 TGTCTCAACATGTTTTTACGAATATCT 57.785 29.630 8.77 0.00 0.00 1.98
212 213 9.988350 ATGTCTCAACATGTTTTTACGAATATC 57.012 29.630 8.77 0.00 44.51 1.63
216 217 9.605955 CAATATGTCTCAACATGTTTTTACGAA 57.394 29.630 8.77 0.32 42.51 3.85
217 218 8.779303 ACAATATGTCTCAACATGTTTTTACGA 58.221 29.630 8.77 1.73 42.51 3.43
218 219 8.839914 CACAATATGTCTCAACATGTTTTTACG 58.160 33.333 8.77 0.00 42.51 3.18
219 220 9.677567 ACACAATATGTCTCAACATGTTTTTAC 57.322 29.630 8.77 7.60 42.51 2.01
224 225 9.897744 CTTTAACACAATATGTCTCAACATGTT 57.102 29.630 4.92 4.92 45.72 2.71
225 226 8.514594 CCTTTAACACAATATGTCTCAACATGT 58.485 33.333 0.00 0.00 45.72 3.21
226 227 8.729756 TCCTTTAACACAATATGTCTCAACATG 58.270 33.333 1.40 0.00 45.72 3.21
228 229 8.862325 ATCCTTTAACACAATATGTCTCAACA 57.138 30.769 0.00 0.00 42.31 3.33
229 230 8.946085 TGATCCTTTAACACAATATGTCTCAAC 58.054 33.333 0.00 0.00 42.31 3.18
230 231 9.685276 ATGATCCTTTAACACAATATGTCTCAA 57.315 29.630 0.00 0.00 42.31 3.02
231 232 9.330063 GATGATCCTTTAACACAATATGTCTCA 57.670 33.333 0.00 0.00 42.31 3.27
232 233 9.553064 AGATGATCCTTTAACACAATATGTCTC 57.447 33.333 0.00 0.00 42.31 3.36
233 234 9.553064 GAGATGATCCTTTAACACAATATGTCT 57.447 33.333 0.00 0.00 42.31 3.41
234 235 9.553064 AGAGATGATCCTTTAACACAATATGTC 57.447 33.333 0.00 0.00 42.31 3.06
235 236 9.911788 AAGAGATGATCCTTTAACACAATATGT 57.088 29.630 0.00 0.00 46.42 2.29
282 283 9.587772 CGTGGAAGAGAGAGAAATTATAAGAAA 57.412 33.333 0.00 0.00 0.00 2.52
283 284 8.750298 ACGTGGAAGAGAGAGAAATTATAAGAA 58.250 33.333 0.00 0.00 0.00 2.52
284 285 8.294954 ACGTGGAAGAGAGAGAAATTATAAGA 57.705 34.615 0.00 0.00 0.00 2.10
285 286 8.191446 TGACGTGGAAGAGAGAGAAATTATAAG 58.809 37.037 0.00 0.00 0.00 1.73
286 287 8.063200 TGACGTGGAAGAGAGAGAAATTATAA 57.937 34.615 0.00 0.00 0.00 0.98
287 288 7.640597 TGACGTGGAAGAGAGAGAAATTATA 57.359 36.000 0.00 0.00 0.00 0.98
288 289 6.531503 TGACGTGGAAGAGAGAGAAATTAT 57.468 37.500 0.00 0.00 0.00 1.28
289 290 5.977489 TGACGTGGAAGAGAGAGAAATTA 57.023 39.130 0.00 0.00 0.00 1.40
290 291 4.873746 TGACGTGGAAGAGAGAGAAATT 57.126 40.909 0.00 0.00 0.00 1.82
291 292 4.039245 TGTTGACGTGGAAGAGAGAGAAAT 59.961 41.667 0.00 0.00 0.00 2.17
292 293 3.383505 TGTTGACGTGGAAGAGAGAGAAA 59.616 43.478 0.00 0.00 0.00 2.52
293 294 2.956333 TGTTGACGTGGAAGAGAGAGAA 59.044 45.455 0.00 0.00 0.00 2.87
294 295 2.583143 TGTTGACGTGGAAGAGAGAGA 58.417 47.619 0.00 0.00 0.00 3.10
295 296 3.584406 ATGTTGACGTGGAAGAGAGAG 57.416 47.619 0.00 0.00 0.00 3.20
296 297 4.336889 AAATGTTGACGTGGAAGAGAGA 57.663 40.909 0.00 0.00 0.00 3.10
297 298 5.292101 GGATAAATGTTGACGTGGAAGAGAG 59.708 44.000 0.00 0.00 0.00 3.20
298 299 5.046591 AGGATAAATGTTGACGTGGAAGAGA 60.047 40.000 0.00 0.00 0.00 3.10
299 300 5.178797 AGGATAAATGTTGACGTGGAAGAG 58.821 41.667 0.00 0.00 0.00 2.85
300 301 5.160607 AGGATAAATGTTGACGTGGAAGA 57.839 39.130 0.00 0.00 0.00 2.87
301 302 7.279981 TCAATAGGATAAATGTTGACGTGGAAG 59.720 37.037 0.00 0.00 0.00 3.46
302 303 7.065324 GTCAATAGGATAAATGTTGACGTGGAA 59.935 37.037 0.00 0.00 39.21 3.53
303 304 6.537301 GTCAATAGGATAAATGTTGACGTGGA 59.463 38.462 0.00 0.00 39.21 4.02
304 305 6.715464 GTCAATAGGATAAATGTTGACGTGG 58.285 40.000 0.00 0.00 39.21 4.94
308 309 9.113838 AGTGATGTCAATAGGATAAATGTTGAC 57.886 33.333 9.02 9.02 45.34 3.18
319 320 9.298250 GGTAGTATCTTAGTGATGTCAATAGGA 57.702 37.037 5.06 5.06 37.04 2.94
320 321 9.078990 TGGTAGTATCTTAGTGATGTCAATAGG 57.921 37.037 0.00 0.00 36.65 2.57
323 324 9.770097 CAATGGTAGTATCTTAGTGATGTCAAT 57.230 33.333 0.00 0.00 36.65 2.57
324 325 8.758829 ACAATGGTAGTATCTTAGTGATGTCAA 58.241 33.333 0.00 0.00 36.65 3.18
325 326 8.306313 ACAATGGTAGTATCTTAGTGATGTCA 57.694 34.615 0.00 0.00 36.65 3.58
326 327 9.680315 GTACAATGGTAGTATCTTAGTGATGTC 57.320 37.037 0.00 0.00 36.65 3.06
327 328 9.197306 TGTACAATGGTAGTATCTTAGTGATGT 57.803 33.333 0.00 0.00 36.65 3.06
330 331 9.197306 ACATGTACAATGGTAGTATCTTAGTGA 57.803 33.333 0.00 0.00 0.00 3.41
331 332 9.464714 GACATGTACAATGGTAGTATCTTAGTG 57.535 37.037 0.00 0.00 0.00 2.74
332 333 8.639761 GGACATGTACAATGGTAGTATCTTAGT 58.360 37.037 2.19 0.00 0.00 2.24
333 334 8.861086 AGGACATGTACAATGGTAGTATCTTAG 58.139 37.037 11.55 0.00 0.00 2.18
334 335 8.777578 AGGACATGTACAATGGTAGTATCTTA 57.222 34.615 11.55 0.00 0.00 2.10
335 336 7.676683 AGGACATGTACAATGGTAGTATCTT 57.323 36.000 11.55 0.00 0.00 2.40
336 337 8.777578 TTAGGACATGTACAATGGTAGTATCT 57.222 34.615 11.55 0.00 0.00 1.98
339 340 9.650714 ACTATTAGGACATGTACAATGGTAGTA 57.349 33.333 11.55 0.00 0.00 1.82
340 341 8.421784 CACTATTAGGACATGTACAATGGTAGT 58.578 37.037 11.55 8.09 0.00 2.73
341 342 7.385205 GCACTATTAGGACATGTACAATGGTAG 59.615 40.741 11.55 7.50 0.00 3.18
342 343 7.070696 AGCACTATTAGGACATGTACAATGGTA 59.929 37.037 11.55 0.00 0.00 3.25
343 344 6.055588 GCACTATTAGGACATGTACAATGGT 58.944 40.000 11.55 12.47 0.00 3.55
344 345 6.291377 AGCACTATTAGGACATGTACAATGG 58.709 40.000 11.55 11.88 0.00 3.16
345 346 7.170489 CAGAGCACTATTAGGACATGTACAATG 59.830 40.741 11.55 1.63 0.00 2.82
346 347 7.147655 ACAGAGCACTATTAGGACATGTACAAT 60.148 37.037 11.55 10.38 0.00 2.71
347 348 6.154534 ACAGAGCACTATTAGGACATGTACAA 59.845 38.462 11.55 3.12 0.00 2.41
348 349 5.656859 ACAGAGCACTATTAGGACATGTACA 59.343 40.000 11.55 0.00 0.00 2.90
349 350 6.150396 ACAGAGCACTATTAGGACATGTAC 57.850 41.667 0.00 0.00 0.00 2.90
350 351 6.379988 TGAACAGAGCACTATTAGGACATGTA 59.620 38.462 0.00 0.00 0.00 2.29
351 352 5.187772 TGAACAGAGCACTATTAGGACATGT 59.812 40.000 0.00 0.00 0.00 3.21
352 353 5.664457 TGAACAGAGCACTATTAGGACATG 58.336 41.667 0.00 0.00 0.00 3.21
353 354 5.939764 TGAACAGAGCACTATTAGGACAT 57.060 39.130 0.00 0.00 0.00 3.06
354 355 5.939764 ATGAACAGAGCACTATTAGGACA 57.060 39.130 0.00 0.00 0.00 4.02
355 356 8.144478 TCATAATGAACAGAGCACTATTAGGAC 58.856 37.037 0.00 0.00 0.00 3.85
356 357 8.250143 TCATAATGAACAGAGCACTATTAGGA 57.750 34.615 0.00 0.00 0.00 2.94
357 358 8.147058 ACTCATAATGAACAGAGCACTATTAGG 58.853 37.037 0.00 0.00 0.00 2.69
380 381 9.939047 CGCACACTAAAATTCGATTATATACTC 57.061 33.333 0.00 0.00 0.00 2.59
381 382 9.472361 ACGCACACTAAAATTCGATTATATACT 57.528 29.630 0.00 0.00 0.00 2.12
384 385 8.822855 TGAACGCACACTAAAATTCGATTATAT 58.177 29.630 0.00 0.00 0.00 0.86
385 386 8.111836 GTGAACGCACACTAAAATTCGATTATA 58.888 33.333 5.51 0.00 44.51 0.98
386 387 6.959311 GTGAACGCACACTAAAATTCGATTAT 59.041 34.615 5.51 0.00 44.51 1.28
387 388 6.301108 GTGAACGCACACTAAAATTCGATTA 58.699 36.000 5.51 0.00 44.51 1.75
388 389 5.144359 GTGAACGCACACTAAAATTCGATT 58.856 37.500 5.51 0.00 44.51 3.34
389 390 4.378046 GGTGAACGCACACTAAAATTCGAT 60.378 41.667 11.30 0.00 46.96 3.59
390 391 3.059461 GGTGAACGCACACTAAAATTCGA 60.059 43.478 11.30 0.00 46.96 3.71
391 392 3.223157 GGTGAACGCACACTAAAATTCG 58.777 45.455 11.30 0.00 46.96 3.34
392 393 3.561503 GGGTGAACGCACACTAAAATTC 58.438 45.455 11.30 0.00 45.12 2.17
393 394 3.636282 GGGTGAACGCACACTAAAATT 57.364 42.857 11.30 0.00 45.12 1.82
401 402 1.393603 TTGAAATGGGTGAACGCACA 58.606 45.000 1.95 0.00 46.96 4.57
402 403 2.723124 ATTGAAATGGGTGAACGCAC 57.277 45.000 1.95 0.00 44.39 5.34
403 404 2.625314 TGAATTGAAATGGGTGAACGCA 59.375 40.909 2.44 2.44 43.04 5.24
404 405 3.296322 TGAATTGAAATGGGTGAACGC 57.704 42.857 0.00 0.00 0.00 4.84
405 406 6.029607 CAGTATGAATTGAAATGGGTGAACG 58.970 40.000 0.00 0.00 39.69 3.95
406 407 7.156876 TCAGTATGAATTGAAATGGGTGAAC 57.843 36.000 0.00 0.00 45.97 3.18
464 466 5.125097 CACGTGTTCCCTAATCTACTGTACT 59.875 44.000 7.58 0.00 0.00 2.73
465 467 5.338365 CACGTGTTCCCTAATCTACTGTAC 58.662 45.833 7.58 0.00 0.00 2.90
466 468 4.400251 CCACGTGTTCCCTAATCTACTGTA 59.600 45.833 15.65 0.00 0.00 2.74
467 469 3.194968 CCACGTGTTCCCTAATCTACTGT 59.805 47.826 15.65 0.00 0.00 3.55
468 470 3.194968 ACCACGTGTTCCCTAATCTACTG 59.805 47.826 15.65 0.00 0.00 2.74
599 604 2.710377 AGATTGCTATGCGTTTGACCA 58.290 42.857 0.00 0.00 0.00 4.02
600 605 3.764885 AAGATTGCTATGCGTTTGACC 57.235 42.857 0.00 0.00 0.00 4.02
613 618 4.489306 AGGAGTACCTACCAAAGATTGC 57.511 45.455 0.00 0.00 45.83 3.56
632 638 0.248907 CGTGGCGGTGTATGAGTAGG 60.249 60.000 0.00 0.00 0.00 3.18
732 925 5.507315 CCATCGTGGGAAAGTATATTTTGCC 60.507 44.000 20.13 20.13 45.59 4.52
734 927 5.067153 TGCCATCGTGGGAAAGTATATTTTG 59.933 40.000 0.00 0.00 33.84 2.44
735 928 5.197451 TGCCATCGTGGGAAAGTATATTTT 58.803 37.500 6.23 0.00 33.84 1.82
739 932 2.104111 CCTGCCATCGTGGGAAAGTATA 59.896 50.000 6.23 0.00 37.44 1.47
770 963 2.233676 TGCCGATGCTTTTGTAGAGAGA 59.766 45.455 0.00 0.00 38.71 3.10
877 1072 0.037877 TTCGTCTTCCTCTCCGGTCT 59.962 55.000 0.00 0.00 0.00 3.85
901 1102 1.091771 CACGAGCAGGCGAATTGGAT 61.092 55.000 0.00 0.00 34.83 3.41
904 1105 1.577328 AACCACGAGCAGGCGAATTG 61.577 55.000 0.00 0.00 34.83 2.32
946 1147 1.234821 GAATCAAGACCGCCACACAA 58.765 50.000 0.00 0.00 0.00 3.33
954 1155 1.415374 AACACGACGAATCAAGACCG 58.585 50.000 0.00 0.00 0.00 4.79
1195 1405 1.161563 GCGACGGAGAGGAGTAGGAG 61.162 65.000 0.00 0.00 0.00 3.69
1268 1478 1.859427 CTTCTTCGGGTGGTCGTCGA 61.859 60.000 0.00 0.00 0.00 4.20
1286 1496 1.201429 ATCCCCAAACGAGGACAGCT 61.201 55.000 0.00 0.00 34.20 4.24
1290 1500 0.107654 CCAGATCCCCAAACGAGGAC 60.108 60.000 0.00 0.00 34.20 3.85
1389 1599 5.163258 GGTGTTGGAGATGAAGATGAGGTAT 60.163 44.000 0.00 0.00 0.00 2.73
1737 1950 1.497991 CGAACTTCTTCTTGTCCGCA 58.502 50.000 0.00 0.00 0.00 5.69
1771 1984 2.465774 CGATGAACGCCATGGACAA 58.534 52.632 18.40 0.00 35.17 3.18
1840 2053 2.885644 GATGATGTCGCGCGTGGT 60.886 61.111 30.98 16.33 0.00 4.16
2163 2376 2.915659 ACGTCGCTGAGAACCCCA 60.916 61.111 0.00 0.00 0.00 4.96
2390 2616 4.397103 CAGATCAACAAATAGCTGAGCCAA 59.603 41.667 0.00 0.00 29.17 4.52
2424 2650 2.252127 ATTCCCAACGAATGCACGCG 62.252 55.000 3.53 3.53 39.84 6.01
2492 2719 6.313905 CGTAGCAAAACCATACAGATTTCTCT 59.686 38.462 0.00 0.00 0.00 3.10
2610 2837 7.998767 CGAGTAACTATAATGCTGAAATTCGTG 59.001 37.037 0.00 0.00 0.00 4.35
2639 2866 2.049526 CACGCTGACACTACGGCA 60.050 61.111 0.00 0.00 41.65 5.69
2750 2977 9.194716 CAGTTCGAAACGTATACAATGTTTATG 57.805 33.333 0.00 0.00 45.34 1.90
2751 2978 8.928733 ACAGTTCGAAACGTATACAATGTTTAT 58.071 29.630 0.00 0.00 45.34 1.40
2752 2979 8.296799 ACAGTTCGAAACGTATACAATGTTTA 57.703 30.769 0.00 0.00 45.34 2.01
2754 2981 6.774354 ACAGTTCGAAACGTATACAATGTT 57.226 33.333 0.00 0.00 39.05 2.71
2755 2982 6.201425 ACAACAGTTCGAAACGTATACAATGT 59.799 34.615 0.00 0.00 36.23 2.71
2818 3051 4.709886 AGTTCCAATTTTATTCCTTCGGGG 59.290 41.667 0.00 0.00 35.37 5.73
2847 3080 4.448732 GTGGCCAAAGTCAAATAAAAGCAG 59.551 41.667 7.24 0.00 0.00 4.24
2866 3099 1.230324 GTCTGTCCTGAAACAGTGGC 58.770 55.000 4.15 0.00 45.57 5.01
2870 3103 4.013267 AGGAATGTCTGTCCTGAAACAG 57.987 45.455 0.00 0.00 44.14 3.16
2878 3111 3.096092 ACTCTCTCAGGAATGTCTGTCC 58.904 50.000 0.00 0.00 36.25 4.02
2886 3119 3.697045 CGTAACAGGACTCTCTCAGGAAT 59.303 47.826 0.00 0.00 0.00 3.01
2900 4370 4.353737 CAATTGATTGATGCCGTAACAGG 58.646 43.478 0.00 0.00 40.14 4.00
2967 4437 6.986817 CGAGAACTCCTAATGTTCCATGTATT 59.013 38.462 0.00 0.00 43.28 1.89
3003 4473 8.760980 TGAGAACTCCTAATCCTTTTCAAAAA 57.239 30.769 0.00 0.00 0.00 1.94
3004 4474 8.796475 CATGAGAACTCCTAATCCTTTTCAAAA 58.204 33.333 0.00 0.00 0.00 2.44
3005 4475 8.163408 TCATGAGAACTCCTAATCCTTTTCAAA 58.837 33.333 0.00 0.00 0.00 2.69
3006 4476 7.607991 GTCATGAGAACTCCTAATCCTTTTCAA 59.392 37.037 0.00 0.00 0.00 2.69
3007 4477 7.106239 GTCATGAGAACTCCTAATCCTTTTCA 58.894 38.462 0.00 0.00 0.00 2.69
3008 4478 7.106239 TGTCATGAGAACTCCTAATCCTTTTC 58.894 38.462 0.00 0.00 0.00 2.29
3009 4479 7.020827 TGTCATGAGAACTCCTAATCCTTTT 57.979 36.000 0.00 0.00 0.00 2.27
3010 4480 6.627087 TGTCATGAGAACTCCTAATCCTTT 57.373 37.500 0.00 0.00 0.00 3.11
3011 4481 6.409005 CCATGTCATGAGAACTCCTAATCCTT 60.409 42.308 14.67 0.00 0.00 3.36
3012 4482 5.071519 CCATGTCATGAGAACTCCTAATCCT 59.928 44.000 14.67 0.00 0.00 3.24
3013 4483 5.163258 ACCATGTCATGAGAACTCCTAATCC 60.163 44.000 14.67 0.00 0.00 3.01
3014 4484 5.757320 CACCATGTCATGAGAACTCCTAATC 59.243 44.000 14.67 0.00 0.00 1.75
3019 4489 3.340814 ACACCATGTCATGAGAACTCC 57.659 47.619 14.67 0.00 0.00 3.85
3043 4513 2.289820 CAGAATGGAATGGATCAGCACG 59.710 50.000 0.00 0.00 0.00 5.34
3150 4621 2.690497 CTGGTATGTGAGGACGACTGAT 59.310 50.000 0.00 0.00 0.00 2.90
3244 4715 0.661483 GACGTTCTGCTTTTGCCTGC 60.661 55.000 0.00 0.00 46.87 4.85


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.